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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ), 'gf_id' => 'HOM05D001207', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001207' ), 'data_identifier' => 'HOM05D001207', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001207', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p27820' => 'bna', 'A05p15070' => 'bna', 'A05p15110' => 'bna', 'A06p30040' => 'bna', 'A06p39520' => 'bna', 'A08p09620' => 'bna', 'A09p04250' => 'bna', 'A09p08220' => 'bna', 'Aa31LG1G18630' => 'aar', 'Aa31LG2G4940' => 'aar', 'Aa31LG3G14110' => 'aar', 'Aa31LG3G5780' => 'aar', 'Aa31sc222G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3523' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1402' => 'aag', 'Actinidia08861' => 'ach', 'Actinidia09671' => 'ach', 'Actinidia25218' => 'ach', 'Actinidia25593' => 'ach', 'Actinidia29405' => 'ach', 'Actinidia33249' => 'ach', 'Actinidia36798' => 'ach', 'Actinidia38703' => 'ach', 'Ah.02g115310' => 'amhyb', 'Ah.05g178730' => 'amhyb', 'Ah.11g040880' => 'amhyb', 'AL7G44010' => 'aly', 'AL8G19830' => 'aly', 'AL8G24490' => 'aly', 'AL8G40460' => 'aly', 'Aqoxy3G01479' => 'aox', 'Aqoxy5G02631' => 'aox', 'Aqoxy5G03471' => 'aox', 'Aqoxy7G02296' => 'aox', 'arahy.Tifrunner.gnm1.ann1.439XX2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52ATST' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HFL4GJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6TRL0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7FYSY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q2MK8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1AFU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBA1JX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1JR8G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V9HKJ8' => 'arhy', 'AT5G35170' => 'ath', 'AT5G47840' => 'ath', 'AT5G50370' => 'ath', 'AT5G63400' => 'ath', 'ATR0629G027' => 'atr', 'ATR0686G103' => 'atr', 'ATR1136G076' => 'atr', 'Atru.chr11.2281' => 'acertr', 'Atru.chr13.2333' => 'acertr', 'Atru.chr7.251' => 'acertr', 'Atru.chr9.1090' => 'acertr', 'AUR62004586' => 'cqu', 'AUR62011265' => 'cqu', 'AUR62023533' => 'cqu', 'AUR62025914' => 'cqu', 'AUR62029641' => 'cqu', 'AUR62041441' => 'cqu', 'AUR62043763' => 'cqu', 'BcaB01g02895' => 'bca', 'BcaB04g18058' => 'bca', 'BcaB04g19536' => 'bca', 'BcaB04g19914' => 'bca', 'BcaC01g02586' => 'bca', 'BcaC01g04808' => 'bca', 'BcaC04g23324' => 'bca', 'BcaC04g23325' => 'bca', 'BcaC04g23805' => 'bca', 'BcaC07g37674' => 'bca', 'BolC3t15676H' => 'bol', 'BolC3t18572H' => 'bol', 'BolC7t44394H' => 'bol', 'BolC8t48045H' => 'bol', 'BolC9t53379H' => 'bol', 'BolC9t53842H' => 'bol', 'BraA03t11993Z' => 'bra', 'BraA06t25956Z' => 'bra', 'BraA06t26867Z' => 'bra', 'BraA08t32959Z' => 'bra', 'BraA09t36062Z' => 'bra', 'BraA09t36473Z' => 'bra', 'C03p33550' => 'bna', 'C03p63170' => 'bna', 'C07p38750' => 'bna', 'C09p04490' => 'bna', 'C09p09290' => 'bna', 'CAN.G1194.14' => 'can', 'CAN.G1647.6' => 'can', 'CAN.G195.9' => 'can', 'CAN.G2.6' => 'can', 'CAN.G352.31' => 'can', 'CAN.G444.3' => 'can', 'CAN.G551.23' => 'can', 'CANSAT01G2479' => 'cansat', 'CANSAT11G0601' => 'cansat', 'CANSAT25G2196' => 'cansat', 'CANSAT80G0785' => 'cansat', 'CARHR184380' => 'chi', 'CARHR217250' => 'chi', 'CARHR258120' => 'chi', 'CARHR277230' => 'chi', 'Carub.0007s3100' => 'cru', 'Carub.0008s0733' => 'cru', 'Carub.0008s1046' => 'cru', 'Carub.0008s2411' => 'cru', 'Ca_03887_v3' => 'car', 'Ca_19673_v3' => 'car', 'Ca_19675_v3' => 'car', 'Ca_26490_v3' => 'car', 'Ca_29351_v3' => 'car', 'Ca_30990_v3' => 'car', 'CBR_g34141' => 'cbr', 'CBR_g41085' => 'cbr', 'CBR_g41087' => 'cbr', 'Cc04_g09990' => 'ccan', 'Cc06_g07370' => 'ccan', 'Cc10_g11290' => 'ccan', 'CDE05G1386' => 'cde', 'CDE05G3333' => 'cde', 'CDE08G1451' => 'cde', 'CDE10G0689' => 'cde', 'Cfa009346' => 'cfa', 'Cfa012981' => 'cfa', 'Cfa018858' => 'cfa', 'Cfa020877' => 'cfa', 'Cfa022295' => 'cfa', 'Cfa026576' => 'cfa', 'Ciclev10007794m.g' => 'ccl', 'Ciclev10021337m.g' => 'ccl', 'Ciclev10021896m.g' => 'ccl', 'Ciclev10032565m.g' => 'ccl', 'CiPaw.05G113800' => 'cil', 'CiPaw.07G234600' => 'cil', 'CiPaw.11G009800' => 'cil', 'CiPaw.12G037500' => 'cil', 'CiPaw.16G117200' => 'cil', 'ClCG03G003640' => 'cla', 'ClCG06G017760' => 'cla', 'ClCG08G008660' => 'cla', 'ClCG11G003640' => 'cla', 'COL.COLO4_12819' => 'col', 'COL.COLO4_24082' => 'col', 'COL.COLO4_24600' => 'col', 'COL.COLO4_28076' => 'col', 'Cpa.g.c38910' => 'cpa', 'Cpa.g.sc13.148' => 'cpa', 'Cpa.g.sc397.8' => 'cpa', 'Cpa.g.sc397.9' => 'cpa', 'Cpa.g.sc50.8' => 'cpa', 'Cre12.g494850' => 'cre', 'Cre12.g557600' => 'cre', 'CsaV3_1G000690' => 'csa', 'CsaV3_1G009500' => 'csa', 'CsaV3_2G003460' => 'csa', 'CsaV3_6G004680' => 'csa', 'CSS0010390' => 'camsi', 'CSS0016658' => 'camsi', 'CSS0016897' => 'camsi', 'CSS0026722' => 'camsi', 'CSS0028951' => 'camsi', 'CSS0029501' => 'camsi', 'CSS0037904' => 'camsi', 'CSS0042717' => 'camsi', 'CSS0049684' => 'camsi', 'DCAR_007479' => 'dca', 'DCAR_014387' => 'dca', 'DCAR_018904' => 'dca', 'DCAR_019349' => 'dca', 'DCAR_021502' => 'dca', 'DCAR_026217' => 'dca', 'DCAR_031185' => 'dca', 'Dinv04862' => 'din', 'Dinv10982' => 'din', 'Dinv11151' => 'din', 'Dinv15225' => 'din', 'Dinv15226' => 'din', 'Dinv41783' => 'din', 'Dinv42907' => 'din', 'Dinv43194' => 'din', 'Duzib068G0202' => 'dzi', 'Duzib084G1110' => 'dzi', 'Duzib168G0412' => 'dzi', 'Duzib177G0274' => 'dzi', 'Duzib177G0286' => 'dzi', 'Duzib205G1650' => 'dzi', 'Duzib248G0861' => 'dzi', 'ECA234G4327' => 'eca', 'ECA246G1243' => 'eca', 'EL10Ac1g00150' => 'bvu', 'EL10Ac8g18828' => 'bvu', 'EL10As4g23425' => 'bvu', 'Eucgr.B00131' => 'egr', 'Eucgr.C00416' => 'egr', 'Eucgr.F02985' => 'egr', 'Eucgr.K02740' => 'egr', 'FAN04G1545' => 'fan', 'FAN08G3152' => 'fan', 'FAN08G3308' => 'fan', 'FAN13G0914' => 'fan', 'FAN18G0437' => 'fan', 'FAN18G3416' => 'fan', 'FAN19G3000' => 'fan', 'FAN23G1325' => 'fan', 'FAN26G2247' => 'fan', 'FvH4_5g07870' => 'fve', 'FvH4_5g31400' => 'fve', 'Glyma.05G046100' => 'gma', 'Glyma.05G046300' => 'gma', 'Glyma.06G171800' => 'gma', 'Glyma.09G096800' => 'gma', 'Glyma.09G234300' => 'gma', 'Glyma.15G203100' => 'gma', 'Glyma.17G128300' => 'gma', 'Gohir.A01G155600' => 'ghi', 'Gohir.A05G275600' => 'ghi', 'Gohir.A06G048800' => 'ghi', 'Gohir.A07G052300' => 'ghi', 'Gohir.A08G156600' => 'ghi', 'Gohir.A09G246400' => 'ghi', 'Gohir.A12G078644' => 'ghi', 'Gohir.A12G188400' => 'ghi', 'Gohir.D01G154500' => 'ghi', 'Gohir.D05G277700' => 'ghi', 'Gohir.D06G048500' => 'ghi', 'Gohir.D07G056800' => 'ghi', 'Gohir.D09G247000' => 'ghi', 'Gohir.D12G191066' => 'ghi', 'Gorai.001G060300' => 'gra', 'Gorai.002G191300' => 'gra', 'Gorai.006G271500' => 'gra', 'Gorai.008G205200' => 'gra', 'Gorai.009G290700' => 'gra', 'Gorai.010G054600' => 'gra', 'GSVIVG01001035001' => 'vvi', 'GSVIVG01008505001' => 'vvi', 'GSVIVG01010361001' => 'vvi', 'GSVIVG01026008001' => 'vvi', 'HanXRQChr02g0040571' => 'han', 'HanXRQChr03g0061281' => 'han', 'HanXRQChr05g0153941' => 'han', 'HanXRQChr06g0174951' => 'han', 'HanXRQChr06g0175661' => 'han', 'HanXRQChr10g0278341' => 'han', 'HanXRQChr10g0318251' => 'han', 'HanXRQChr11g0347101' => 'han', 'Haze_07242' => 'cav', 'Haze_19308' => 'cav', 'Haze_21345' => 'cav', 'Haze_21351' => 'cav', 'Haze_26806' => 'cav', 'Haze_26916' => 'cav', 'Hma1.2p1_0014F.1_g009700' => 'hma', 'Hma1.2p1_0182F.1_g080600' => 'hma', 'Hma1.2p1_0342F.1_g130690' => 'hma', 'Hma1.2p1_1954F.1_g308880' => 'hma', 'HPP92_003741' => 'vpl', 'HPP92_003780' => 'vpl', 'HPP92_003781' => 'vpl', 'HPP92_003856' => 'vpl', 'HPP92_003923' => 'vpl', 'HPP92_023203' => 'vpl', 'HPP92_024231' => 'vpl', 'HPP92_024249' => 'vpl', 'Hund02423' => 'sun', 'Hund10183' => 'sun', 'Hund16768' => 'sun', 'Lalb_Chr01g0000151' => 'lal', 'Lalb_Chr06g0172021' => 'lal', 'Lalb_Chr07g0183291' => 'lal', 'Lalb_Chr08g0237051' => 'lal', 'Lalb_Chr11g0069661' => 'lal', 'Lalb_Chr12g0202121' => 'lal', 'Lalb_Chr13g0297381' => 'lal', 'Lalb_Chr23g0275791' => 'lal', 'Lj1g0011916' => 'lja', 'Lj3A1065G87' => 'lonja', 'Lj3g0019948' => 'lja', 'Lj4g0007215' => 'lja', 'Lj5A97G89' => 'lonja', 'Lj5g0002827' => 'lja', 'Lj6A823G48' => 'lonja', 'Lj7C286G4' => 'lonja', 'Lj9A710G64' => 'lonja', 'Lsat_1_v5_gn_1_9700' => 'lsa', 'Lsat_1_v5_gn_3_29621' => 'lsa', 'Lsat_1_v5_gn_4_76541' => 'lsa', 'Lsat_1_v5_gn_5_13541' => 'lsa', 'Lsat_1_v5_gn_5_90580' => 'lsa', 'Lsat_1_v5_gn_6_30540' => 'lsa', 'Lsat_1_v5_gn_8_149620' => 'lsa', 'Manes.02G199500' => 'mes', 'Manes.06G117800' => 'mes', 'Manes.13G016600' => 'mes', 'Manes.14G053400' => 'mes', 'Manes.14G139700' => 'mes', 'Mapoly0019s0102' => 'mpo', 'Mapoly0139s0019' => 'mpo', 'MBI03_g18681_MAGBIO' => 'mbi', 'MBI19_g20936_MAGBIO' => 'mbi', 'MBI19_g42085_MAGBIO' => 'mbi', 'MCO03G541' => 'mco', 'MCO04G223' => 'mco', 'MCO07G091' => 'mco', 'MCO07G664' => 'mco', 'MCO15G697' => 'mco', 'MCO16G216' => 'mco', 'MD02G1012500' => 'mdo', 'MD06G1145300' => 'mdo', 'MD08G1217400' => 'mdo', 'MD11G1173700' => 'mdo', 'MD14G1160000' => 'mdo', 'MD15G1404700' => 'mdo', 'Medtr2g461290' => 'mtr', 'Medtr4g035170' => 'mtr', 'Medtr4g103800' => 'mtr', 'MELO3C002349.2' => 'cme', 'MELO3C004452.2' => 'cme', 'MELO3C019938.2' => 'cme', 'MELO3C026227.2' => 'cme', 'Migut.C01276' => 'egut', 'Migut.D01244' => 'egut', 'Migut.I00516' => 'egut', 'Migut.K00366' => 'egut', 'MSTRG.11287' => 'ama', 'MSTRG.1532' => 'ama', 'MSTRG.22908' => 'ama', 'MSTRG.25453' => 'ama', 'MSTRG.26312' => 'ama', 'Nitab4.5_0000148g0020' => 'nta', 'Nitab4.5_0000365g0110' => 'nta', 'Nitab4.5_0000955g0030' => 'nta', 'Nitab4.5_0001579g0020' => 'nta', 'Nitab4.5_0001664g0010' => 'nta', 'Nitab4.5_0001751g0080' => 'nta', 'Nitab4.5_0003103g0020' => 'nta', 'Nitab4.5_0003680g0040' => 'nta', 'Nitab4.5_0005330g0050' => 'nta', 'Nitab4.5_0013256g0010' => 'nta', 'Nn3g16525' => 'nnu', 'Nn4g22388' => 'nnu', 'Nn5g27424' => 'nnu', 'Nn8g39732' => 'nnu', 'Oeu000541.2' => 'oeu', 'Oeu001896.1' => 'oeu', 'Oeu019044.1' => 'oeu', 'Oeu023477.1' => 'oeu', 'Oeu040777.3' => 'oeu', 'Oeu045462.1' => 'oeu', 'Oeu052210.1' => 'oeu', 'Oeu052212.1' => 'oeu', 'Oeu064083.1' => 'oeu', 'Os08g0109300' => 'osa', 'Os08g0288200' => 'osa', 'Os11g0312220' => 'osa', 'Os11g0312400' => 'osa', 'Os12g0236400' => 'osa', 'Peaxi162Scf00089g00431' => 'pax', 'Peaxi162Scf00128g01038' => 'pax', 'Peaxi162Scf00177g00814' => 'pax', 'Peaxi162Scf00391g00320' => 'pax', 'Peaxi162Scf00536g00311' => 'pax', 'PGR042G3019' => 'pgr', 'PGR044G1994' => 'pgr', 'PGR083G2753' => 'pgr', 'PGR142G3550' => 'pgr', 'PGSC0003DMG400001247' => 'stu', 'PGSC0003DMG400013933' => 'stu', 'PGSC0003DMG400015187' => 'stu', 'PGSC0003DMG400026110' => 'stu', 'Phvul.003G209400' => 'pvu', 'Phvul.009G208900' => 'pvu', 'Phvul.011G003000' => 'pvu', 'Potri.006G189201' => 'ptr', 'Potri.012G095300' => 'ptr', 'Potri.013G103400' => 'ptr', 'Potri.015G092800' => 'ptr', 'Potri.018G113400' => 'ptr', 'Potri.019G078200' => 'ptr', 'Pp3c11_11060' => 'ppa', 'Pp3c11_22230' => 'ppa', 'Pp3c23_18090' => 'ppa', 'Pp3c23_18091' => 'ppa', 'Pp3c27_6280' => 'ppa', 'Pp3c2_28130' => 'ppa', 'Pp3c6_20610' => 'ppa', 'PRCOL_00002653' => 'pco', 'PRCOL_00003652' => 'pco', 'PRCOL_00006083' => 'pco', 'PRCOL_00006173' => 'pco', 'Prupe.1G556600' => 'ppe', 'Prupe.5G153600' => 'ppe', 'Prupe.7G253500' => 'ppe', 'Psat0s1799g0080' => 'psa', 'Psat1g022840' => 'psa', 'Psat4g064040' => 'psa', 'Psat7g192360' => 'psa', 'PSO017G2539' => 'pso', 'PSO017G4960' => 'pso', 'PSO017G6918' => 'pso', 'PSO170G5208' => 'pso', 'PSO384G0626' => 'pso', 'PSO478G5263' => 'pso', 'PSO591G0151' => 'pso', 'PSO832G4471' => 'pso', 'QL02p023752' => 'qlo', 'QL02p091447' => 'qlo', 'QL03p054555' => 'qlo', 'QL03p054560' => 'qlo', 'QL10p004376' => 'qlo', 'RcHm_v2.0_Chr1g0329011' => 'rch', 'RcHm_v2.0_Chr2g0086531' => 'rch', 'RcHm_v2.0_Chr2g0147601' => 'rch', 'RcHm_v2.0_Chr4g0434501' => 'rch', 'RcHm_v2.0_Chr5g0017821' => 'rch', 'RcHm_v2.0_Chr7g0187191' => 'rch', 'RcHm_v2.0_Chr7g0190591' => 'rch', 'RcHm_v2.0_Chr7g0223711' => 'rch', 'RcHm_v2.0_Chr7g0226671' => 'rch', 'Rhsim03G0254100' => 'rsi', 'Rhsim11G0052000' => 'rsi', 'Rhsim11G0052100' => 'rsi', 'Rhsim12G0104400' => 'rsi', 'Rhsim12G0173500' => 'rsi', 'Sabra12G0070000' => 'sbr', 'Sabra13G0089500' => 'sbr', 'Sabra15G0114500' => 'sbr', 'Sabra19G0089200' => 'sbr', 'SalBow5G2671' => 'sbo', 'Sc04g0000760' => 'sci', 'Sc08g0004930' => 'sci', 'Sc23g0001590' => 'sci', 'Sed0001389' => 'sed', 'Sed0003003' => 'sed', 'Sed0004457' => 'sed', 'Sed0016283' => 'sed', 'Sed0025573' => 'sed', 'SEGI_07636' => 'sgi', 'SEGI_19852' => 'sgi', 'SGA_v2.0_scaffold118G32543' => 'sas', 'SGA_v2.0_scaffold161G37777' => 'sas', 'SGA_v2.0_scaffold183G39863' => 'sas', 'SGA_v2.0_scaffold215G42340' => 'sas', 'SGA_v2.0_scaffold40G15655' => 'sas', 'SGA_v2.0_scaffold5G02874' => 'sas', 'SMO147G0349' => 'smo', 'SMO198G0006' => 'smo', 'SMO356G0649' => 'smo', 'SMO358G0192' => 'smo', 'SMO364G0753' => 'smo', 'Solyc03g111200.3' => 'sly', 'Solyc05g014980.4' => 'sly', 'Solyc06g065270.4' => 'sly', 'Solyc12g010380.3' => 'sly', 'Sopen05g010070' => 'spe', 'Sopen06g023770' => 'spe', 'Sopen11g010480' => 'spe', 'Sopen12g005390' => 'spe', 'Sp2g18340' => 'spa', 'Sp2g26490' => 'spa', 'Sp6g12520' => 'spa', 'Sp7g07210' => 'spa', 'SpUn0015_0140' => 'spa', 'SpUn0050_0020' => 'spa', 'TAR374G1367' => 'tar', 'TAR622G1233' => 'tar', 'TAR628G0728' => 'tar', 'TAR629G3125' => 'tar', 'TAR636G0058' => 'tar', 'TAR636G2435' => 'tar', 'THA.LOC104798951' => 'tha', 'THA.LOC104807203' => 'tha', 'THA.LOC104811598' => 'tha', 'THA.LOC104825011' => 'tha', 'Thecc.02G275500' => 'tca', 'Thecc.03G126100' => 'tca', 'Thecc.08G173100' => 'tca', 'Thecc.09G142600' => 'tca', 'Thhalv10003444m.g' => 'esa', 'Thhalv10004711m.g' => 'esa', 'Thhalv10004716m.g' => 'esa', 'Thhalv10004838m.g' => 'esa', 'Thhalv10014224m.g' => 'esa', 'TPR.G10955' => 'tpr', 'TPR.G15464' => 'tpr', 'TPR.G22801' => 'tpr', 'TPR.G31920' => 'tpr', 'TWI14G0327' => 'twi', 'TWI14G1107' => 'twi', 'TWI34G1792' => 'twi', 'TWI36G0855' => 'twi', 'TWI36G1157' => 'twi', 'TWI39G0434' => 'twi', 'unitig_62.g23479' => 'ugi', 'unitig_747.g21329' => 'ugi', 'vmacro00740' => 'vma', 'vmacro00741' => 'vma', 'vmacro06110' => 'vma', 'vmacro16127' => 'vma', 'vmacro16666' => 'vma', 'vmacro19220' => 'vma', 'vmacro20927' => 'vma', 'VMungo0720G1864' => 'vmu', 'VMungo1127G0008' => 'vmu', 'VMungo1215G2150' => 'vmu', 'VMungo1215G3398' => 'vmu', 'VMungo1309G0472' => 'vmu', 'Zm00001eb109850' => 'zma', 'Zm00001eb133450' => 'zma', 'Zm00001eb158850' => 'zma', 'Zm00001eb177670' => 'zma', 'Zm00001eb239710' => 'zma', 'Zm00001eb260410' => 'zma', 'Zm00001eb370400' => 'zma', 'Zm00001eb411760' => 'zma' ) $gf_id = 'HOM05D001207' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001207' ) $data_identifier = 'HOM05D001207' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 7, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 9, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 7, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 9, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb411760' $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